Many microfabrication processes require the formation of device structures on opposing sides of a substrate, such as a semiconductor wafer or layer. In one conventional microfabrication process, an image of alignment marks on a first mask is captured during the formation of first device structures in a first surface of the substrate using the first mask and photolithographic processing techniques. Then, during the formation of second device structures in a second surface of the substrate, an alignment step is performed indirectly based on the captured image rather than directly from a mask. During this alignment step, the captured image is aligned to alignment marks on the second surface. Unfortunately, this indirect alignment process may not provide sufficient alignment accuracy for applications requiring a high degree of alignment between the first and second device structures on opposing sides of a substrate (e.g., semiconductor wafer).